def __init__(self, elems, epsilon=None):
"""elems should contain metapost knots or links"""
if epsilon is None:
epsilon = _epsilon
knots = []
is_closed = True
for i, elem in enumerate(elems):
if isinstance(elem, _link):
elem.set_knots(elems[i - 1], elems[(i + 1) % len(elems)])
elif isinstance(elem, _knot):
knots.append(elem)
if elem.ltype == mp_endpoint or elem.rtype == mp_endpoint:
is_closed = False
# link the knots among each other
for i in range(len(knots)):
knots[i - 1].next = knots[i]
# determine the control points
mp_make_choices(knots[0], epsilon)
pathmodule.path.__init__(self)
# build up the path
do_moveto = True
do_lineto = False
do_curveto = False
prev = None
for i, elem in enumerate(elems):
if isinstance(elem, _link):
do_moveto = False
if isinstance(elem, line):
do_lineto, do_curveto = True, False
else:
do_lineto, do_curveto = False, True
elif isinstance(elem, _knot):
if do_moveto:
self.append(pathmodule.moveto_pt(elem.x_pt, elem.y_pt))
if do_lineto:
self.append(pathmodule.lineto_pt(elem.x_pt, elem.y_pt))
elif do_curveto:
self.append(
pathmodule.curveto_pt(prev.rx_pt, prev.ry_pt,
elem.lx_pt, elem.ly_pt,
elem.x_pt, elem.y_pt))
do_moveto = True
do_lineto = False
do_curveto = False
prev = elem
# close the path if necessary
if knots[0].ltype == mp_explicit:
elem = knots[0]
if do_lineto and is_closed:
self.append(pathmodule.closepath())
elif do_curveto:
self.append(
pathmodule.curveto_pt(prev.rx_pt, prev.ry_pt, elem.lx_pt,
elem.ly_pt, elem.x_pt, elem.y_pt))
if is_closed:
self.append(pathmodule.closepath())
class ProteinDomain(Brick):
_default_color = cmyk.Purple
_offset = (0, -0.5)
_path = path(
moveto(0, 0),
lineto(1, 0),
lineto(1, 1),
lineto(0, 1),
lineto(0, 0),
closepath(),
moveto(1.4, 0),
lineto(2.4, 0),
lineto(2.4, 1),
lineto(1.4, 1),
lineto(1.4, 0),
closepath(),
moveto(2.8, 0),
lineto(4, 0),
lineto(4, -0.5),
lineto(4+sqrt(3), 0.5),
lineto(4, 1.5),
lineto(4, 1),
lineto(2.8, 1),
lineto(2.8, 0),
closepath()
)
def __init__(self, elems, epsilon=None):
"""elems should contain metapost knots or links"""
if epsilon is None:
epsilon = _epsilon
knots = []
is_closed = True
for i, elem in enumerate(elems):
if isinstance(elem, _link):
elem.set_knots(elems[i-1], elems[(i+1)%len(elems)])
elif isinstance(elem, _knot):
knots.append(elem)
if elem.ltype == mp_endpoint or elem.rtype == mp_endpoint:
is_closed = False
# link the knots among each other
for i in range(len(knots)):
knots[i-1].next = knots[i]
# determine the control points
mp_make_choices(knots[0], epsilon)
pathmodule.path.__init__(self)
# build up the path
do_moveto = True
do_lineto = False
do_curveto = False
prev = None
for i, elem in enumerate(elems):
if isinstance(elem, _link):
do_moveto = False
if isinstance(elem, line):
do_lineto, do_curveto = True, False
else:
do_lineto, do_curveto = False, True
elif isinstance(elem, _knot):
if do_moveto:
self.append(pathmodule.moveto_pt(elem.x_pt, elem.y_pt))
if do_lineto:
self.append(pathmodule.lineto_pt(elem.x_pt, elem.y_pt))
elif do_curveto:
self.append(pathmodule.curveto_pt(prev.rx_pt, prev.ry_pt, elem.lx_pt, elem.ly_pt, elem.x_pt, elem.y_pt))
do_moveto = True
do_lineto = False
do_curveto = False
prev = elem
# close the path if necessary
if knots[0].ltype == mp_explicit:
elem = knots[0]
if do_lineto and is_closed:
self.append(pathmodule.closepath())
elif do_curveto:
self.append(pathmodule.curveto_pt(prev.rx_pt, prev.ry_pt, elem.lx_pt, elem.ly_pt, elem.x_pt, elem.y_pt))
if is_closed:
self.append(pathmodule.closepath())
def draw_sector(self, end):
"""draw the sector"""
segment = path.path(
path.arc(self.xo, self.yo, self.inner_r, self.start_angle,
self.end_angle),
path.arcn(self.xo, self.yo, self.sector_width + self.inner_r,
self.end_angle, self.start_angle), path.closepath())
self.shape_canvas.fill(segment, [self.sector_color])
# draw a delimiting line between sectors
line_color = color.gray(0.15)
if end and (self.end_angle - self.start_angle) < 0.25:
line_color = color.rgb.red
r = self.inner_r + self.sector_width
start_radians = self.start_angle * pi / 180.0
end_radians = self.end_angle * pi / 180.0
x0 = self.inner_r * cos(start_radians) + self.xo
y0 = self.inner_r * sin(start_radians) + self.yo
x1 = r * cos(start_radians) + self.xo
y1 = r * sin(start_radians) + self.yo
self.shape_canvas.stroke(path.line(x0, y0, x1, y1),
[style.linewidth(0.01), line_color])
x0 = self.inner_r * cos(end_radians) + self.xo
y0 = self.inner_r * sin(end_radians) + self.yo
x1 = r * cos(end_radians) + self.xo
y1 = r * sin(end_radians) + self.yo
self.shape_canvas.stroke(path.line(x0, y0, x1, y1),
[style.linewidth(0.01), line_color])
def corner(nx, ny, z, facecolor, edgecolor, trans, xdir, ydir):
if xdir:
p = path.path(path.moveto(*projector(nx, z, ny)),
path.lineto(*projector(nx - 1, z, ny)),
path.lineto(*projector(nx - 1, z + 1, ny)),
path.lineto(*projector(nx, z + 1, ny)), path.closepath())
c.fill(p, [facecolor, color.transparency(trans)])
if ydir:
p = path.path(path.moveto(*projector(nx, z, ny)),
path.lineto(*projector(nx, z, ny + 1)),
path.lineto(*projector(nx, z + 1, ny + 1)),
path.lineto(*projector(nx, z + 1, ny)), path.closepath())
c.fill(p, [facecolor, color.transparency(trans)])
x0, y0 = projector(nx, z, ny)
x1, y1 = projector(nx, z + 1, ny)
c.stroke(path.line(x0, y0, x1, y1), [edgecolor])
def state(x0, y0, r, c):
x1 = x0 - r / sqrt(2)
y1 = y0 + r / sqrt(2)
x2 = x0 - 3 * r / 4 / sqrt(2)
y2 = y1 + r / 8
x3 = x0 - r / 4 / sqrt(2)
y3 = y1 - r / 8
x4 = x0 + r / 4 / sqrt(2)
y4 = y1 + r / 8
x5 = x0 + 3 * r / 4 / sqrt(2)
y5 = y1 - r / 8
x6 = x0 + r / sqrt(2)
y6 = y1
delta = r / 40
c.fill(path.circle(x0, y0, r), [color.cmyk.RoyalBlue])
c.fill(path.rect(x1 + delta, y0 + delta,
r * sqrt(2) - 2 * delta, r), [color.rgb.white])
inside = path.curve(x1, y1, x2, y2, x3, y3, x0, y1) << \
path.curve(x0, y1, x4, y4, x5, y5, x6, y6) << \
path.line(x6, y6, x6, y0) << \
path.line(x6, y0, x1, y0)
inside.append(path.closepath())
c.fill(inside, [color.cmyk.RoyalBlue])
c.stroke(path.circle(x0, y0, r), [style.linewidth(r / 25)])
def signature(self, deg_max=6, padded=False, has_border=False):
""" For a visualization of glyphs, lay out in a 2D grid PNG file. """
self.scale()
sig = canvas.canvas([trafo.rotate(90), trafo.mirror(0)])
scale = 1.5
if padded or has_border:
sig_margin = 0.2
x = (deg_max + 1) * scale + (1.5 * sig_margin)
border_path = path.path(path.moveto(0, 0), path.lineto(0, x),
path.lineto(x, x), path.lineto(x, 0),
path.closepath())
if padded:
border_color = color.cmyk.White
if has_border:
border_color = color.cmyk.Gray
sig.stroke(border_path, [
border_color,
trafo.translate(-sig_margin * 2, -sig_margin * 2),
style.linewidth(.025)
])
for index in self.glist:
if len(index) > 2:
c = degree_glyph(index[0], index[1], index[2],
(self.mincount, self.maxcount))
else:
c = degree_glyph(index[0], index[1], 1,
(self.mincount, self.maxcount))
sig.insert(c,
[trafo.translate(index[0] * scale, (index[1]) * scale)
]) # text writing requires full latex
return sig
def paint(self, canvas, data, axis, axispos):
if self.breaklinesattrs is not None:
breaklinesdist_pt = unit.topt(self.breaklinesdist)
breaklineslength_pt = unit.topt(self.breaklineslength)
breaklinesextent_pt = (0.5*breaklinesdist_pt*math.fabs(self.cos) +
0.5*breaklineslength_pt*math.fabs(self.sin))
if canvas.extent_pt < breaklinesextent_pt:
canvas.extent_pt = breaklinesextent_pt
for v in [data.subaxes[name].vminover for name in data.names[1:]]:
# use a tangent of the basepath (this is independent of the tickdirection)
p = axispos.vbasepath(v, None).normpath()
breakline = p.tangent(0, length=self.breaklineslength)
widthline = p.tangent(0, length=self.breaklinesdist).transformed(trafomodule.rotate(self.breaklinesangle+90, *breakline.atbegin()))
# XXX Uiiii
tocenter = map(lambda x: 0.5*(x[0]-x[1]), zip(breakline.atbegin(), breakline.atend()))
towidth = map(lambda x: 0.5*(x[0]-x[1]), zip(widthline.atbegin(), widthline.atend()))
breakline = breakline.transformed(trafomodule.translate(*tocenter).rotated(self.breaklinesangle, *breakline.atbegin()))
breakline1 = breakline.transformed(trafomodule.translate(*towidth))
breakline2 = breakline.transformed(trafomodule.translate(-towidth[0], -towidth[1]))
canvas.fill(path.path(path.moveto_pt(*breakline1.atbegin_pt()),
path.lineto_pt(*breakline1.atend_pt()),
path.lineto_pt(*breakline2.atend_pt()),
path.lineto_pt(*breakline2.atbegin_pt()),
path.closepath()), [color.gray.white])
canvas.stroke(breakline1, self.defaultbreaklinesattrs + self.breaklinesattrs)
canvas.stroke(breakline2, self.defaultbreaklinesattrs + self.breaklinesattrs)
_title.paint(self, canvas, data, axis, axispos)
def place(self, x, y):
x0, y0 = self.coords[0]
paths = [path.moveto(x + x0, y + y0)]
for point in self.coords[1:]:
paths.append(path.lineto(x + point[0], y + point[1]))
paths.append(path.closepath())
return (path.path(*paths), self.color, self.stroke_color)
def paint(self, canvas, data, axis, axispos):
if self.breaklinesattrs is not None:
breaklinesdist_pt = unit.topt(self.breaklinesdist)
breaklineslength_pt = unit.topt(self.breaklineslength)
breaklinesextent_pt = (0.5*breaklinesdist_pt*math.fabs(self.cos) +
0.5*breaklineslength_pt*math.fabs(self.sin))
if canvas.extent_pt < breaklinesextent_pt:
canvas.extent_pt = breaklinesextent_pt
for v in [data.subaxes[name].vminover for name in data.names[1:]]:
# use a tangent of the basepath (this is independent of the tickdirection)
p = axispos.vbasepath(v, None).normpath()
breakline = p.tangent(0, length=self.breaklineslength)
widthline = p.tangent(0, length=self.breaklinesdist).transformed(trafomodule.rotate(self.breaklinesangle+90, *breakline.atbegin()))
# XXX Uiiii
tocenter = map(lambda x: 0.5*(x[0]-x[1]), zip(breakline.atbegin(), breakline.atend()))
towidth = map(lambda x: 0.5*(x[0]-x[1]), zip(widthline.atbegin(), widthline.atend()))
breakline = breakline.transformed(trafomodule.translate(*tocenter).rotated(self.breaklinesangle, *breakline.atbegin()))
breakline1 = breakline.transformed(trafomodule.translate(*towidth))
breakline2 = breakline.transformed(trafomodule.translate(-towidth[0], -towidth[1]))
canvas.layer("baseline").fill(path.path(path.moveto_pt(*breakline1.atbegin_pt()),
path.lineto_pt(*breakline1.atend_pt()),
path.lineto_pt(*breakline2.atend_pt()),
path.lineto_pt(*breakline2.atbegin_pt()),
path.closepath()), [color.gray.white])
canvas.layer("baseline").stroke(breakline1, self.defaultbreaklinesattrs + self.breaklinesattrs)
canvas.layer("baseline").stroke(breakline2, self.defaultbreaklinesattrs + self.breaklinesattrs)
_title.paint(self, canvas, data, axis, axispos)
class Promoter(Brick):
_default_color = cmyk.ForestGreen
_offset = (0, -0.5)
_path = path(moveto(0, 0), lineto(1, 0), lineto(1, 0.75), lineto(3, 0.75),
lineto(3, 0.25), lineto(3 + sqrt(3) * 0.75, 1.125),
lineto(3, 2.0), lineto(3, 1.5), lineto(1, 1.5),
curveto(0.5, 1.5, 0.125, 1.5, 0, 1), lineto(0, 0),
closepath())
def dopath(ps, extra=[], fill=[], closepath=True, smooth=0.3):
ps = [path.moveto(*ps[0])]+[path.lineto(*p) for p in ps[1:]]
if closepath:
ps.append(path.closepath())
p = path.path(*ps)
if fill:
c.fill(p, [deformer.smoothed(smooth)]+extra+fill)
c.stroke(p, [deformer.smoothed(smooth)]+extra)
def dopath(ps, extra=[], fill=False, closepath=True):
ps = [path.moveto(*ps[0])]+[path.lineto(*p) for p in ps[1:]]
if closepath:
ps.append(path.closepath())
p = path.path(*ps)
if fill:
c.fill(p, [deformer.smoothed(0.3)]+extra+[color.rgb.white])
c.stroke(p, [deformer.smoothed(0.3)]+extra)
def server(r, servercolor=color.rgb(0.5, 0.5, 0.8)):
c = canvas.canvas()
c.fill(path.circle(0, 0, r), [servercolor, trafo.scale(1, 0.5)])
h = 2 * r
p = path.path(path.moveto(-r, 0), path.lineto(-r, -h),
path.arc(0, -h, r, 180, 0), path.lineto(r, 0),
path.arcn(0, 0, r, 0, 180), path.closepath())
c.fill(p, [servercolor, trafo.scale(1, 0.5).translated(0, -0.08 * r)])
return c
def corner(nx, ny, z, facecolor, edgecolor, trans, xdir, ydir):
if xdir:
p = path.path(path.moveto(*projector(nx, z, ny)),
path.lineto(*projector(nx-1, z, ny)),
path.lineto(*projector(nx-1, z+1, ny)),
path.lineto(*projector(nx, z+1, ny)),
path.closepath())
c.fill(p, [facecolor, color.transparency(trans)])
if ydir:
p = path.path(path.moveto(*projector(nx, z, ny)),
path.lineto(*projector(nx, z, ny+1)),
path.lineto(*projector(nx, z+1, ny+1)),
path.lineto(*projector(nx, z+1, ny)),
path.closepath())
c.fill(p, [facecolor, color.transparency(trans)])
x0, y0 = projector(nx, z, ny)
x1, y1 = projector(nx, z+1, ny)
c.stroke(path.line(x0, y0, x1, y1), [edgecolor])
def polygonal_path(Z, loop=True):
pa = path.path( path.moveto(Z[0].real, Z[0].imag),
path.multilineto_pt(
[ ( unit.topt(z.real), unit.topt(z.imag) )
for z in Z[1:] ] ))
if loop:
pa.append(path.closepath())
return pa
def client(clientcolor=color.rgb(0.8, 0.5, 0.5)):
c = canvas.canvas()
r = 0.3
c.fill(path.circle(0, 0, r), [clientcolor])
r = 0.5
p = path.path(path.moveto(-r, 0), path.curveto(-r, r, r, r, r, 0),
path.closepath())
c.fill(p, [clientcolor, trafo.translate(0, -1.3 * r)])
return c
def read(size, color):
size = size * 0.25
cread = canvas.canvas()
cread.fill(path.circle(0, 0, 0.35), [color, trafo.scale(size)])
p = path.path(path.moveto(0.8, 0),
path.curveto(0.2, 0.5, -0.2, 0.5, -0.8, 0),
path.curveto(-0.2, -0.5, 0.2, -0.5, 0.8, 0),
path.closepath())
cread.stroke(p, [color, style.linewidth.thick, trafo.scale(size)])
return cread
def draw_pie(c, radius, start, end):
pie = path.path(path.moveto(0, 0), path.arc(0, 0, radius, start, end),
path.closepath())
hue = (start + end) / (360 * 2)
color = pyx.color.hsb(hue, 0.8, 0.8)
c.stroke(
pie,
[style.linewidth(0.01),
pyx.color.rgb(1, 1, 1),
deco.filled([color])])
def write(size, color):
size = size * 0.3
cwrite = canvas.canvas()
p = path.path(path.moveto(-0.2, 0.8), path.lineto(0.2, 0.8),
path.lineto(0.2, 0), path.lineto(0, -0.2),
path.lineto(-0.2, 0), path.lineto(-0.2, 0.8),
path.closepath(), path.moveto(0, 0.8), path.lineto(0, 0.05),
path.moveto(-0.2, 0), path.arcn(-0.1, 0, 0.1, 180, 20),
path.arcn(0.1, 0, 0.1, 160, 0))
cwrite.stroke(
p, [color,
trafo.scale(size).rotated(-30).translated(0, -0.4 * size)])
return cwrite
def arrow(x0, y0, x1, y1):
alpha = 0.3
beta = 0.5
x2 = x1 + (x1 - x0) * alpha
y2 = y1 + (y1 - y0) * alpha
x3 = x2 + (y1 - y0) * beta
y3 = y2 + (x0 - x1) * beta
x4 = x2 - (y1 - y0) * beta
y4 = y2 - (x0 - x1) * beta
arrow = path.line(x0, y0, x3, y3) << path.line(
x3, y3, x1, y1) << path.line(x1, y1, x4, y4)
arrow.append(path.closepath())
return arrow
def draw(self):
p = path.path(path.moveto(*self.corners[0]),
path.lineto(*self.corners[1]),
path.lineto(*self.corners[2]),
path.lineto(*self.corners[3]),
path.closepath())
fillcolor = color.hsb(2/3*(1-(self.counter-1)/(self.nsquares-1)), 0.2, 1)
self.c.stroke(p, [deco.filled([fillcolor])])
x, y = 0.5*(self.corners[0]+self.corners[2])
s = int(np.sum(np.abs(self.corners[1]-self.corners[0])))
self.c.text(x, y, str(s),
[text.halign.center, text.valign.middle,
text.size(min(s, 5))])
self.counter = self.counter+1
def dopath(ps, extra=[], fill=[], closepath=False, smooth=0.0):
if not ps:
print "dopath: empty"
return
ps = [path.moveto(*ps[0])]+[path.lineto(*p) for p in ps[1:]]
if closepath:
ps.append(path.closepath())
p = path.path(*ps)
extra = list(extra)
if smooth:
extra.append(deformer.smoothed(smooth))
if fill:
c.fill(p, extra+fill)
c.stroke(p, extra)
def frontplane(z, nxmax, mymax, facecolor, edgecolor, trans):
p = path.path(path.moveto(*projector(0, z, 0)),
path.lineto(*projector(nxmax, z, 0)),
path.lineto(*projector(nxmax, z, nymax)),
path.lineto(*projector(0, z, nymax)), path.closepath())
c.fill(p, [facecolor, color.transparency(trans)])
c.stroke(p, [edgecolor])
for nx in range(1, nxmax):
x0, y0 = projector(nx, z, 0)
x1, y1 = projector(nx, z, nymax)
c.stroke(path.line(x0, y0, x1, y1), [edgecolor])
for ny in range(1, nymax):
x0, y0 = projector(0, z, ny)
x1, y1 = projector(nxmax, z, ny)
c.stroke(path.line(x0, y0, x1, y1), [edgecolor])
def draw(self):
p = path.path(path.moveto(*self.corners[0]),
path.lineto(*self.corners[1]),
path.lineto(*self.corners[2]),
path.lineto(*self.corners[3]), path.closepath())
fillcolor = color.hsb(
2 / 3 * (1 - (self.counter - 1) / (self.nsquares - 1)), 0.2, 1)
self.c.stroke(p, [deco.filled([fillcolor])])
x, y = 0.5 * (self.corners[0] + self.corners[2])
s = int(np.sum(np.abs(self.corners[1] - self.corners[0])))
self.c.text(
x, y, str(s),
[text.halign.center, text.valign.middle,
text.size(min(s, 5))])
self.counter = self.counter + 1
def test_pie(radius, start, end):
c = canvas.canvas()
container = path.rect(-(radius + 1), -(radius + 1), 2 * (radius + 1),
2 * (radius + 1))
c.stroke(container, [style.linewidth(0.001), color.rgb.red])
pie = path.path(path.moveto(0, 0), path.arc(0, 0, radius, start, end),
path.closepath())
c.stroke(pie, [
style.linewidth(0.1),
pyx.color.rgb(1, 1, 1),
deco.filled([color.rgb.red])
])
c.writeSVGfile("figure")
def frontplane(z, nxmax, mymax, facecolor, edgecolor, trans):
p = path.path(path.moveto(*projector(0, z, 0)),
path.lineto(*projector(nxmax, z, 0)),
path.lineto(*projector(nxmax, z, nymax)),
path.lineto(*projector(0, z, nymax)),
path.closepath())
c.fill(p, [facecolor, color.transparency(trans)])
c.stroke(p, [edgecolor])
for nx in range(1, nxmax):
x0, y0 = projector(nx, z, 0)
x1, y1 = projector(nx, z, nymax)
c.stroke(path.line(x0, y0, x1, y1), [edgecolor])
for ny in range(1, nymax):
x0, y0 = projector(0, z, ny)
x1, y1 = projector(nxmax, z, ny)
c.stroke(path.line(x0, y0, x1, y1), [edgecolor])
def draw_drop(x, y, r, c):
c.fill(path.circle(x, y - 3 * r, r), [color.cmyk.RoyalBlue])
c.stroke(path.circle(x, y - 3 * r, r))
triangle = path.line(
x, y, x + sqrt(8) * r / 3, y - 8 * r / 3) << path.line(
x + sqrt(8) * r / 3, y - 8 * r / 3, x - sqrt(8) * r / 3,
y - 8 * r / 3)
triangle.append(path.closepath())
c.fill(triangle, [color.cmyk.RoyalBlue])
c.stroke(
path.line(x - sqrt(8) * r / 3, y -
8 * r / 3, x, y) << path.line(x, y, x + sqrt(8) * r / 3, y -
8 * r / 3))
c.fill(path.circle(x - 0.5 * r, (y - 3 * r) / 2, 0.2 * r),
[color.rgb.white, trafo.scale(sx=1, sy=2)])
def plot(self, canvas, shape="s"):
"""Plot this direction on a pyx canvas.
The direction will be transformed onto a Lambert equal-area
projection and plotted as a square, circle, or triangle
(shape parameter: s, c, or t).
"""
(x, y) = self.project()
if shape == "s":
canvas.stroke(path.rect(x - 0.1, y - 0.1, 0.2, 0.2))
elif shape == "t":
s = 0.15
canvas.stroke(path.path(path.moveto(x, y + s),
path.rlineto(-0.866 * s, -1.5 * s),
path.rlineto(2 * .866 * s, 0),
path.closepath()))
elif shape == "c":
canvas.stroke(path.circle(x, y, 0.1))
def file(c, size=1, xoff=0, yoff=0, attrs=[], title=''):
w = 3
h = 2.1
fold = 0.6
outline = path.path(path.moveto(0, 0), path.lineto(w, 0),
path.lineto(w, h - fold), path.lineto(w - fold, h),
path.lineto(0, h), path.closepath())
foldpath = path.path(path.moveto(w - fold, h),
path.lineto(w - fold, h - fold),
path.lineto(w, h - fold))
c1 = canvas.canvas()
c1.stroke(outline, attrs)
d = deformer.smoothed(0.2)
c1.stroke(d.deform(foldpath), attrs)
c1.stroke(path.rect(0.1 * w, 0.3 * h, 0.6 * w, 0.1 * h))
c1.stroke(path.rect(0.1 * w, 0.45 * h, 0.6 * w, 0.1 * h))
c1.stroke(path.rect(0.1 * w, 0.6 * h, 0.6 * w, 0.1 * h))
c1.stroke(path.rect(0.1 * w, 0.75 * h, 0.6 * w, 0.1 * h))
c1.text(0.1, 0.1, r'\sffamily ' + title, [trafo.scale(0.7)])
myattrs = [trafo.translate(xoff, yoff), trafo.scale(size)]
myattrs.extend(attrs)
c.insert(c1, myattrs)
def interpolated_path(Z, shape=1.0, loop=True):
shape /= 6.0
I = range(0, len(Z)-2)
if loop:
I += [-1]
segments = [ ( Z[i] + (Z[i+1]-Z[i-1])*shape,
Z[i+1] - (Z[i+2]-Z[i])*shape,
Z[i+1] )
for i in I ]
pa = path.path( path.moveto(Z[0].real, Z[0].imag),
path.multicurveto_pt(
[ (unit.topt(W[0].real), unit.topt(W[0].imag),
unit.topt(W[1].real), unit.topt(W[1].imag),
unit.topt(W[2].real), unit.topt(W[2].imag) )
for W in segments ]))
if loop:
pa.append(path.closepath())
return pa
def zvgridpath(self, vz):
return path.path(path.moveto_pt(*self.vpos_pt(0, 0, vz)),
path.lineto_pt(*self.vpos_pt(1, 0, vz)),
path.lineto_pt(*self.vpos_pt(1, 1, vz)),
path.lineto_pt(*self.vpos_pt(0, 1, vz)),
path.closepath())
def yvgridpath(self, vy):
return path.path(path.moveto_pt(*self.vpos_pt(0, vy, 0)),
path.lineto_pt(*self.vpos_pt(1, vy, 0)),
path.lineto_pt(*self.vpos_pt(1, vy, 1)),
path.lineto_pt(*self.vpos_pt(0, vy, 1)),
path.closepath())
def xvgridpath(self, vx):
return path.path(path.moveto_pt(*self.vpos_pt(vx, 0, 0)),
path.lineto_pt(*self.vpos_pt(vx, 1, 0)),
path.lineto_pt(*self.vpos_pt(vx, 1, 1)),
path.lineto_pt(*self.vpos_pt(vx, 0, 1)),
path.closepath())
def plot_memory(data, width, height):
plot_width = width - 4.0
plot_height = height - 0.8
left_width = plot_width * 0.6
right_width = plot_width * 0.2
prob = data['HiFive-Probability']['3']
norm = data['HiCNorm']['3']
prob_min = prob - right_width * 2.2e4 / left_width * 0.7
prob_max = prob + right_width * 2.2e4 / left_width * 0.3
norm_min = norm - right_width * 2.2e4 / left_width * 0.6
norm_max = norm + right_width * 2.2e4 / left_width * 0.4
c1 = canvas.canvas()
g1 = graph.graphxy(width=left_width, height=plot_height,
y=graph.axis.nestedbar(painter=graph.axis.painter.bar(nameattrs=None)),
x=graph.axis.lin(painter=painter, texter=graph.axis.texter.exponential(mantissaexp=r"{{%s}e%s}", nomantissaexp=r"{e%s}"), min=0, max=2.2e4),
x2=graph.axis.lin(parter=None, min=0, max=1),
y2=graph.axis.lin(painter=None, min=0, max=1))
c1.insert(g1, [trafo.translate(0, 0)])
g2 = graph.graphxy(width=right_width, height=plot_height,
y=graph.axis.lin(painter=None, min=0, max=1),
x=graph.axis.lin(painter=painter, texter=graph.axis.texter.exponential(mantissaexp=r"{{%s}e%s}", nomantissaexp=r"{e%s}"), min=prob_min, max=prob_max),
x2=graph.axis.lin(parter=None, min=0, max=1),
y2=graph.axis.lin(painter=None, min=0, max=1))
c1.insert(g2, [trafo.translate(left_width, 0)])
g3 = graph.graphxy(width=right_width, height=plot_height,
y=graph.axis.lin(painter=None, min=0, max=1),
x=graph.axis.lin(painter=painter, texter=graph.axis.texter.exponential(mantissaexp=r"{{%s}e%s}", nomantissaexp=r"{e%s}"), parter=graph.axis.parter.linear(tickdists=[5000]), min=norm_min, max=norm_max),
x2=graph.axis.lin(parter=None, min=0, max=1),
y2=graph.axis.lin(parter=None, min=0, max=1))
c1.insert(g3, [trafo.translate(left_width + right_width, 0)])
split = canvas.canvas()
split.fill(path.path(path.moveto(-0.15, -0.2), path.lineto(0.05, 0.2), path.lineto(.15, 0.2),
path.lineto(-0.05, -0.2), path.closepath()), [color.cmyk.White])
split.stroke(path.line(-0.15, -0.2, 0.05, 0.2))
split.stroke(path.line(-0.05, -0.2, 0.15, 0.2))
c1.insert(split, [trafo.translate(left_width, 0)])
c1.insert(split, [trafo.translate(left_width, plot_height)])
c1.insert(split, [trafo.translate(left_width + right_width, 0)])
c1.insert(split, [trafo.translate(left_width + right_width, plot_height)])
methods = ['HiCLib', 'HiCPipe', 'HiCNorm', 'HiFive-Probability', 'HiFive-Binning', 'HiFive-Express',
'HiFive-ExpressKR', 'HiFive-ExpressKR w/distance']
hstep = plot_height / len(methods)
substep = hstep / 6.0
scale = left_width / 2.2e4
for i, meth in enumerate(methods[::-1]):
for j in range(5):
if str(j) not in data[meth]:
continue
if meth not in ['HiCNorm', 'HiFive-Probability'] or j != 3:
c1.fill(path.rect(0, hstep * i + (4.5 - j) * substep, data[meth][str(j)] * scale, substep),
[step_colors[j]])
elif meth == 'HiCNorm':
c1.fill(path.rect(0, hstep * i + (4.5 - j) * substep, left_width + right_width * 1.7, substep),
[step_colors[j]])
c1.insert(split, [trafo.translate(left_width, hstep * i + (5 - j) * substep)])
c1.insert(split, [trafo.translate(left_width + right_width, hstep * i + (5 - j) * substep)])
else:
c1.fill(path.rect(0, hstep * i + (4.5 - j) * substep, left_width + right_width * 0.6, substep),
[step_colors[j]])
c1.insert(split, [trafo.translate(left_width, hstep * i + (5 - j) * substep)])
c = canvas.canvas()
c.insert(c1, [trafo.translate(4.0, 0.8)])
for i, meth in enumerate(methods):
c.text(3.9, height - plot_height / len(methods) * (i + 0.5), meth,
[text.halign.right, text.valign.middle, text.size(-2)])
c.text(4.0 + plot_width / 2, 0, "Maximum RAM usage (resident set size, Mbytes)",
[text.halign.center, text.valign.bottom, text.size(-2)])
return c
def polygon(*points): # pragma: no cover
args = []
for i, point in enumerate(points):
args.append(path.moveto(*point) if i == 0 else path.lineto(*point))
args.append(path.closepath())
return path.path(*args)
axislen = 3
text.set(engine=text.LatexEngine)
text.preamble(r'''\usepackage[sfdefault,scaled=.85]{FiraSans}
\usepackage{newtxsf}
\usepackage{nicefrac}''')
unit.set(vscale=1.2, wscale=1.3, xscale=1.3)
c = canvas.canvas()
c.stroke(path.line(-0.2*axislen, 0, axislen, 0), [deco.earrow])
c.text(axislen+0.1, 0, 'Re($x$)', [text.valign.middle])
c.stroke(path.line(0, -0.2*axislen, 0, axislen), [deco.earrow])
c.text(0.2, axislen, 'Im($x$)', [text.valign.top])
r = 0.85*axislen
p = path.path(path.moveto(0, 0),
path.lineto(r, 0),
path.arc(0, 0, r, 0, 45),
path.lineto(0, 0),
path.closepath())
pathcolor = color.rgb(0.2, 0, 0.8)
c.stroke(p, [style.linewidth.thick, style.linejoin.round, pathcolor])
c.stroke(path.line(0, 0, 0.53*axislen, 0), [deco.earrow, pathcolor])
c.stroke(path.path(path.arc(0, 0, r, 0, 23)), [deco.earrow, pathcolor])
c.stroke(path.path(path.moveto(r/sqrt(2), r/sqrt(2)),
path.lineto(0.48*r/sqrt(2), 0.48*r/sqrt(2))),
[deco.earrow, pathcolor])
c.text(0.33, 0.11, r'\footnotesize$\nicefrac{\pi}{4}$', [pathcolor])
c.stroke(path.path(path.arc(0, 0, 0.82, 0, 45)),
[style.linewidth.thin, pathcolor])
c.writePDFfile()
def xvgridpath(self, vx):
return path.path(path.moveto_pt(*self.vpos_pt(vx, 0, 0)),
path.lineto_pt(*self.vpos_pt(vx, 1, 0)),
path.lineto_pt(*self.vpos_pt(vx, 1, 1)),
path.lineto_pt(*self.vpos_pt(vx, 0, 1)),
path.closepath())
def plot_scores(self,
fname,
binsize=10000,
show_lads=False,
show_dips=False,
show_means=False,
show_partitions=False):
"""Plot a PDF of score data with optional indicators of partitions, "
partition means, LADs, and DIPs."""
# Make sure that the PYX module is available
try:
from pyx import canvas, path, document, color, text, style
except ImportError:
self.logger.warn("The package pyx must be installed to plot data")
return None
# Make sure desired data is present
if self.focus != 'binned':
if (self.data is None or numpy.nanmin(self.data['score']) == 0):
self.logger.warn("Requested data is not available for "
"plotting")
return None
elif (self.binned is None or numpy.nanmin(self.binned['score']) == 0):
self.logger.warn("Requested binned data is not available for "
"plotting")
return None
self.logger.info("Plotting data")
# Determine which data to use
if self.focus == 'binned':
data = self.binned
chr_indices = self.bin_indices
else:
data = self.data
chr_indices = self.chr_indices
# Plot each chromosome on its own page
pages = []
for i in range(self.chroms.shape[0]):
valid = numpy.where(
numpy.logical_not(
numpy.isnan(
data['score'][chr_indices[i]:chr_indices[i + 1]])))[0]
valid += chr_indices[i]
# Skip chromosomes without valid data
if valid.shape[0] == 0:
continue
mids = (data['coords'][valid, 0] + data['coords'][valid, 1]) // 2
if binsize > 0:
# Bin data to the resolution requested
start = (mids[0] // binsize) * binsize
stop = (mids[-1] // binsize + 1) * binsize
indices = (mids - start) // binsize
counts = numpy.bincount(indices)
Ys = numpy.bincount(
indices, weights=data['score'][valid]) / numpy.maximum(
1, counts)
mids = (start + numpy.arange(
(stop - start) // binsize) * binsize + binsize / 2)
valid = numpy.where(counts > 0)[0]
Ys = Ys[valid]
mids = mids[valid]
coords = numpy.zeros((Ys.shape[0], 2), dtype=numpy.float64)
coords[:, 0] = start + valid * binsize
coords[:, 1] = start + valid * binsize + binsize
else:
Ys = data['score'][valid]
start = data['coords'][valid, 0]
stop = data['coords'][valid[-1], 1]
coords = data['coords'][valid, :].astype(numpy.float64)
c = canvas.canvas()
width = (stop - start) / 5000000.
height = 5.
maxscore = numpy.amax(numpy.abs(Ys))
if show_means and self.partitions is not None:
where = numpy.where(self.partitions['chr'] == i)[0]
maxscore = max(
maxscore,
numpy.amax(numpy.abs(self.partitions['score'][where])))
Ys /= maxscore
Ys *= height * 0.5
Xs = (mids - start) / float(stop - start) * width
coords -= start
coords /= (stop - start)
coords *= width
lpath = path.path(path.moveto(0, 0))
for j in range(valid.shape[0]):
if j == 0 or valid[j] - valid[j - 1] > 1:
lpath.append(path.lineto(coords[j, 0], 0))
lpath.append(path.lineto(Xs[j], Ys[j]))
if j == Xs.shape[0] - 1 or valid[j + 1] - valid[j] > 1:
lpath.append(path.lineto(coords[j, 1], 0))
lpath.append(path.lineto(width, 0))
lpath.append(path.closepath())
# add lads if requests and already determined
if show_lads and self.LADs is not None:
where = numpy.where(self.LADs['chr'] == i)[0]
if where.shape[0] == 0:
continue
for j in where:
X0 = ((self.LADs['coords'][j, 0] - start) /
float(stop - start) * width)
X1 = ((self.LADs['coords'][j, 1] - start) /
float(stop - start) * width)
c.fill(path.rect(X0, -height / 2, X1 - X0, height),
[color.gray(0.85)])
# add dips if requests and already determined
if show_dips and self.DIPs is not None:
print(self.DIPs.shape)
where = numpy.where(self.DIPs['chr'] == i)[0]
if where.shape[0] == 0:
continue
for j in where:
X0 = ((self.DIPs['coords'][j, 0] - start) /
float(stop - start) * width)
X1 = ((self.DIPs['coords'][j, 1] - start) /
float(stop - start) * width)
c.fill(path.rect(X0, -height / 2, X1 - X0, height),
[color.rgb.red])
# add signal track
c.fill(lpath)
c.stroke(path.line(0, -height / 2, width, -height / 2))
# add partition mean line if requested and already determined
if show_means and self.partitions is not None:
where = numpy.where(self.partitions['chr'] == i)[0]
coords = ((self.partitions['coords'][where, :] - start) /
float(stop - start) * width)
Ys = ((self.partitions['score'][where] / maxscore) * height *
0.5)
lpath = path.path(path.moveto(0, 0))
for j in range(Ys.shape[0]):
if j == 0 or coords[j, 0] != coords[j - 1, 1]:
lpath.append(path.lineto(coords[j, 0], 0))
lpath.append(path.lineto(coords[j, 0], Ys[j]))
lpath.append(path.lineto(coords[j, 1], Ys[j]))
if (j == Ys.shape[0] - 1
or coords[j, 1] != coords[j + 1, 0]):
lpath.append(path.lineto(coords[j, 1], 0))
lpath.append(path.lineto(width, 0))
c.stroke(lpath, [
color.rgb.blue, style.linewidth.THIN,
color.transparency(0.5)
])
# add partition lines if requested and already determined
if show_partitions and self.partitions is not None:
where = numpy.where(self.partitions['chr'] == i)[0]
coords = ((self.partitions['coords'][where, :] - start) /
float(stop - start) * width)
for j in range(coords.shape[0] - 1):
c.stroke(
path.line(coords[j, 1], -height * 0.5, coords[j, 1],
height * 0.5), [style.linewidth.THin])
if coords[j, 1] != coords[j + 1, 0]:
c.stroke(
path.line(coords[j + 1, 0], -height * 0.5,
coords[j + 1, 0], height * 0.5),
[style.linewidth.THin])
# add coordinates
for j in range(int(numpy.ceil(start / 10000000.)),
int(numpy.floor(stop / 10000000.) + 1)):
X = (j * 10000000. - start) / (stop - start) * width
c.stroke(path.line(X, -height / 2, X, -height / 2 - 0.2))
c.text(X, -height / 2 - 0.25, "%i Mb" % (j * 10),
[text.halign.center, text.valign.top])
c.text(width * 0.5, -height / 2 - 0.6,
"%s" % self.chroms[i].replace('_', ' '),
[text.halign.center, text.valign.top])
pages.append(document.page(c))
doc = document.document(pages)
doc.writePDFfile(fname)
def updatepath(self, path, trafo, context):
path.append(closepath())
# The closepath in T1 is different from PostScripts in that it does
# *not* modify the current position; hence we need to add an additional
# moveto here ...
path.append(moveto_pt(*trafo.apply_pt(context.x, context.y)))
def plot_bargraph(data, width, height):
methods = ['HiCLib', 'HiCPipe', 'HiCNorm', 'HiFive-Probability', 'HiFive-Binning', 'HiFive-Express',
'HiFive-ExpressKR', 'HiFive-ExpressKR w/distance']
ho = 4.0
left_width = (width - ho) * 0.45
mid_width1 = (width - ho) * 0.3
mid_width2 = (width - ho) * 0.125
right_width = (width - ho) * 0.125
bar_height = height / len(methods) - 0.1
data_totals = {}
ranges = numpy.zeros((4, 2), dtype=numpy.float32)
for meth in data:
data_totals[meth] = find_total(data[meth])
if meth == 'HiCPipe':
ranges[1, 1] = data_totals[meth]
elif meth == 'HiCNorm':
ranges[2, 1] = data_totals[meth]
elif meth == 'HiFive-Probability':
ranges[3, 1] = data_totals[meth]
else:
ranges[0, 1] = max(ranges[0, 1], data_totals[meth])
ranges /= 60.0
ranges[0, 1] = 28.0
ranges[1, 0] = ranges[1, 1] - ranges[0, 1] / 0.45 * 0.3 * 0.9
ranges[1, 1] = ranges[1, 1] + ranges[0, 1] / 0.45 * 0.3 * 0.1
ranges[2, 0] = ranges[2, 1] - ranges[0, 1] / 0.45 * 0.125 * 0.5
ranges[2, 1] = ranges[2, 1] + ranges[0, 1] / 0.45 * 0.125 * 0.5
ranges[3, 0] = ranges[3, 1] - ranges[0, 1] / 0.45 * 0.125 * 0.5
ranges[3, 1] = ranges[3, 1] + ranges[0, 1] / 0.45 * 0.125 * 0.5
c = canvas.canvas()
g1 = graph.graphxy(width=left_width, height=height,
x=graph.axis.lin(painter=painter, min=0, max=ranges[0, 1]),
x2=graph.axis.lin(parter=None, min=0, max=ranges[0, 1]),
y=graph.axis.lin(parter=None, min=0, max=1),
y2=graph.axis.lin(painter=None, min=0, max=1))
c.insert(g1)
g2 = graph.graphxy(width=mid_width1, height=height,
x=graph.axis.lin(painter=painter, min=ranges[1, 0], max=ranges[1, 1]),
x2=graph.axis.lin(parter=None, min=ranges[1, 0], max=ranges[1, 1]),
y2=graph.axis.lin(painter=None, min=0, max=1),
y=graph.axis.lin(painter=None, min=0, max=1))
c.insert(g2, [trafo.translate(left_width, 0)])
g3 = graph.graphxy(width=mid_width2, height=height,
x=graph.axis.lin(painter=painter, min=ranges[2, 0], max=ranges[2, 1]),
x2=graph.axis.lin(parter=None, min=ranges[2, 0], max=ranges[2, 1]),
y2=graph.axis.lin(painter=None, min=0, max=1),
y=graph.axis.lin(painter=None, min=0, max=1))
c.insert(g3, [trafo.translate(left_width + mid_width1, 0)])
g4 = graph.graphxy(width=right_width, height=height,
x=graph.axis.lin(painter=painter, min=ranges[3, 0], max=ranges[3, 1]),
x2=graph.axis.lin(parter=None, min=ranges[3, 0], max=ranges[3, 1]),
y2=graph.axis.lin(parter=None, min=0, max=1),
y=graph.axis.lin(painter=None, min=0, max=1))
c.insert(g4, [trafo.translate(left_width + mid_width1 + mid_width2, 0)])
split = canvas.canvas()
split.fill(path.path(path.moveto(-0.15, -0.2), path.lineto(0.05, 0.2), path.lineto(.15, 0.2),
path.lineto(-0.05, -0.2), path.closepath()), [color.cmyk.White])
split.stroke(path.line(-0.15, -0.2, 0.05, 0.2))
split.stroke(path.line(-0.05, -0.2, 0.15, 0.2))
c.insert(split, [trafo.translate(left_width, 0)])
c.insert(split, [trafo.translate(left_width, height)])
c.insert(split, [trafo.translate(left_width + mid_width1, 0)])
c.insert(split, [trafo.translate(left_width + mid_width1, height)])
c.insert(split, [trafo.translate(left_width + mid_width1 + mid_width2, 0)])
c.insert(split, [trafo.translate(left_width + mid_width1 + mid_width2, height)])
for i, meth in enumerate(methods):
c.insert(plot_bar(data[meth], ranges, bar_height, left_width / ranges[0, 1], split),
[trafo.translate(0, height - 0.05 - bar_height * (i + 1) - i * 0.1)])
c.text(-0.1, height * (len(methods) - i - 0.5) / len(methods), meth,
[text.halign.right, text.valign.middle, text.size(-2)])
c.text((width - ho) / 2.0, -0.35, "Runtime (minutes)",
[text.halign.center, text.valign.top, text.size(-2)])
return c
def polygon(*points): # pragma: no cover
args = []
for i, point in enumerate(points):
args.append(path.moveto(*point) if i == 0 else path.lineto(*point))
args.append(path.closepath())
return path.path(*args)
# prepare the limits of the chart and a clippath
ulx, uly = to_chart_coord(sun_set[0], chart)
urx, ury = to_chart_coord(sun_rise[0], chart)
top_line = path.path(path.moveto(ulx, uly),
path.lineto(urx, ury))
llx, lly = to_chart_coord(sun_set[-1], chart)
lrx, lry = to_chart_coord(sun_rise[-1], chart)
bot_line = path.path(path.moveto(llx, lly),
path.lineto(lrx, lry))
rev_sun_set = sun_set[:]
rev_sun_set.reverse()
clippath = event_to_path(rev_sun_set[:] + sun_rise[:], chart, do_check=False)
clippath.append(path.closepath())
clc = canvas.canvas([canvas.clip(clippath)]) # clipped canvas for paths, text and moon
bclc = canvas.canvas([canvas.clip(clippath)]) # clipped canvas for the background and the dots
# a seperate (larger) clipping canvas for Moon phases
clippath2 = event_to_path([rev_sun_set[0]+2.0] +
rev_sun_set[:] + [rev_sun_set[-1]-2.0], chart, do_check=False,
xoffset=-1.6)
clippath2 = clippath2.joined(event_to_path([sun_rise[0]-2.0] +
sun_rise[:] + [sun_rise[-1]+2.0], chart, do_check=False,
xoffset=1.6))
clippath2.append(path.closepath())
mclc = canvas.canvas([canvas.clip(clippath2)])
make_alm_bg(bclc, begin_day_datetime, no_days, chart,
from pyx import canvas, color, path, text, unit
text.set(text.LatexRunner)
text.preamble(r'\usepackage[sfdefault,scaled=.85,lining]{FiraSans}\usepackage{newtxsf}')
text.preamble(r'\usepackage{nicefrac}')
unit.set(xscale=1.6, wscale=1.2)
c = canvas.canvas()
side = 4
lightcolor = color.hsb(0.65, 0.2, 1)
darkcolor = color.hsb(0.65, 1, 1)
c.fill(path.path(path.moveto(0, 0),
path.lineto(side, 0),
path.arc(0, 0, side, 0, 90),
path.closepath()), [lightcolor])
c.stroke(path.path(path.arc(0, 0, side, 0, 90)), [darkcolor])
c.stroke(path.rect(0, 0, side, side))
ticklen = 0.15
for tick in (0, 1):
dist = tick*side
c.stroke(path.line(dist, 0, dist, -ticklen))
c.text(dist, -1.5*ticklen, str(tick), [text.halign.center, text.valign.top])
c.stroke(path.line(0, dist, -ticklen, dist))
c.text(-1.5*ticklen, dist, str(tick), [text.halign.right, text.valign.middle])
c.text(0.4*side, 0.4*side, r'\huge$\nicefrac{\pi}{4}$',
[text.halign.center, text.valign.middle, darkcolor])
c.writePDFfile()
def plot_bargraph(data, width, height):
methods = [
'HiCLib', 'HiCPipe', 'HiCNorm', 'HiFive-Probability', 'HiFive-Binning',
'HiFive-Express', 'HiFive-ExpressKR', 'HiFive-ExpressKR w/distance'
]
ho = 4.0
left_width = (width - ho) * 0.45
mid_width1 = (width - ho) * 0.3
mid_width2 = (width - ho) * 0.125
right_width = (width - ho) * 0.125
bar_height = height / len(methods) - 0.1
data_totals = {}
ranges = numpy.zeros((4, 2), dtype=numpy.float32)
for meth in data:
data_totals[meth] = find_total(data[meth])
if meth == 'HiCPipe':
ranges[1, 1] = data_totals[meth]
elif meth == 'HiCNorm':
ranges[2, 1] = data_totals[meth]
elif meth == 'HiFive-Probability':
ranges[3, 1] = data_totals[meth]
else:
ranges[0, 1] = max(ranges[0, 1], data_totals[meth])
ranges /= 60.0
ranges[0, 1] = 28.0
ranges[1, 0] = ranges[1, 1] - ranges[0, 1] / 0.45 * 0.3 * 0.9
ranges[1, 1] = ranges[1, 1] + ranges[0, 1] / 0.45 * 0.3 * 0.1
ranges[2, 0] = ranges[2, 1] - ranges[0, 1] / 0.45 * 0.125 * 0.5
ranges[2, 1] = ranges[2, 1] + ranges[0, 1] / 0.45 * 0.125 * 0.5
ranges[3, 0] = ranges[3, 1] - ranges[0, 1] / 0.45 * 0.125 * 0.5
ranges[3, 1] = ranges[3, 1] + ranges[0, 1] / 0.45 * 0.125 * 0.5
c = canvas.canvas()
g1 = graph.graphxy(width=left_width,
height=height,
x=graph.axis.lin(painter=painter,
min=0,
max=ranges[0, 1]),
x2=graph.axis.lin(parter=None, min=0, max=ranges[0, 1]),
y=graph.axis.lin(parter=None, min=0, max=1),
y2=graph.axis.lin(painter=None, min=0, max=1))
c.insert(g1)
g2 = graph.graphxy(width=mid_width1,
height=height,
x=graph.axis.lin(painter=painter,
min=ranges[1, 0],
max=ranges[1, 1]),
x2=graph.axis.lin(parter=None,
min=ranges[1, 0],
max=ranges[1, 1]),
y2=graph.axis.lin(painter=None, min=0, max=1),
y=graph.axis.lin(painter=None, min=0, max=1))
c.insert(g2, [trafo.translate(left_width, 0)])
g3 = graph.graphxy(width=mid_width2,
height=height,
x=graph.axis.lin(painter=painter,
min=ranges[2, 0],
max=ranges[2, 1]),
x2=graph.axis.lin(parter=None,
min=ranges[2, 0],
max=ranges[2, 1]),
y2=graph.axis.lin(painter=None, min=0, max=1),
y=graph.axis.lin(painter=None, min=0, max=1))
c.insert(g3, [trafo.translate(left_width + mid_width1, 0)])
g4 = graph.graphxy(width=right_width,
height=height,
x=graph.axis.lin(painter=painter,
min=ranges[3, 0],
max=ranges[3, 1]),
x2=graph.axis.lin(parter=None,
min=ranges[3, 0],
max=ranges[3, 1]),
y2=graph.axis.lin(parter=None, min=0, max=1),
y=graph.axis.lin(painter=None, min=0, max=1))
c.insert(g4, [trafo.translate(left_width + mid_width1 + mid_width2, 0)])
split = canvas.canvas()
split.fill(
path.path(path.moveto(-0.15, -0.2), path.lineto(0.05, 0.2),
path.lineto(.15, 0.2), path.lineto(-0.05, -0.2),
path.closepath()), [color.cmyk.White])
split.stroke(path.line(-0.15, -0.2, 0.05, 0.2))
split.stroke(path.line(-0.05, -0.2, 0.15, 0.2))
c.insert(split, [trafo.translate(left_width, 0)])
c.insert(split, [trafo.translate(left_width, height)])
c.insert(split, [trafo.translate(left_width + mid_width1, 0)])
c.insert(split, [trafo.translate(left_width + mid_width1, height)])
c.insert(split, [trafo.translate(left_width + mid_width1 + mid_width2, 0)])
c.insert(split,
[trafo.translate(left_width + mid_width1 + mid_width2, height)])
for i, meth in enumerate(methods):
c.insert(
plot_bar(data[meth], ranges, bar_height, left_width / ranges[0, 1],
split),
[
trafo.translate(0, height - 0.05 - bar_height *
(i + 1) - i * 0.1)
])
c.text(-0.1,
height * (len(methods) - i - 0.5) / len(methods), meth,
[text.halign.right, text.valign.middle,
text.size(-2)])
c.text((width - ho) / 2.0, -0.35, "Runtime (minutes)",
[text.halign.center, text.valign.top,
text.size(-2)])
return c
def last_quarter_moon(r, cx, cy) :
p = path.path(path.moveto(cx, cy))
p.append(path.arc(cx, cy, r, 90, -90))
p.append(path.closepath())
return p
def yvgridpath(self, vy):
return path.path(path.moveto_pt(*self.vpos_pt(0, vy, 0)),
path.lineto_pt(*self.vpos_pt(1, vy, 0)),
path.lineto_pt(*self.vpos_pt(1, vy, 1)),
path.lineto_pt(*self.vpos_pt(0, vy, 1)),
path.closepath())
def zvgridpath(self, vz):
return path.path(path.moveto_pt(*self.vpos_pt(0, 0, vz)),
path.lineto_pt(*self.vpos_pt(1, 0, vz)),
path.lineto_pt(*self.vpos_pt(1, 1, vz)),
path.lineto_pt(*self.vpos_pt(0, 1, vz)),
path.closepath())
c.fill(p, [color.grey(0.5), trafo.translate(0.05, -0.05)])
c1 = canvas.canvas([canvas.clip(p)])
c1.fill(p, [color.grey(0.9)])
r = 1
brown1 = color.rgb(148 / 255, 77 / 255, 48 / 255)
brown2 = color.rgb(193 / 255, 91 / 255, 49 / 255)
red1 = color.rgb(200 / 255, 0, 0)
red2 = color.rgb(220 / 255, 0.5, 0.5)
flame = color.rgb(248 / 255, 212 / 255, 27 / 255)
c2 = canvas.canvas()
c2.insert(ellipse(r, 0.5, brown1))
c2.fill(path.rect(-r, 0, 2 * r, 0.5 * r), [brown1])
c2.insert(ellipse(r, 0.5, brown2), [trafo.translate(0, 0.5 * r)])
c2.insert(ellipse(0.2 * r, 0.5, red1), [trafo.translate(0, 0.5 * r)])
c2.fill(path.rect(-0.2 * r, 0.5 * r, 0.4 * r, r), [red1])
c2.insert(ellipse(0.2 * r, 0.5, red2), [trafo.translate(0, 1.5 * r)])
c2.stroke(path.line(0, 1.5 * r, 0, 1.5 * r + 0.2), [style.linewidth.Thick])
c2a = canvas.canvas()
c2a.fill(
path.path(path.moveto(0, 0), path.curveto(-0.1, -0.2, -0.3, -0.6, 0, -0.6),
path.curveto(0.3, -0.6, 0, -0.3, 0, 0), path.closepath()),
[flame])
c2.insert(c2a, [trafo.translate(0, 1.65 * r + 0.6)])
c.insert(c1)
c.insert(c2, [trafo.translate(1.75, 1.3)])
c.insert(c2, [trafo.translate(4.7, 1.3)])
c.writeGSfile(device="png16m", resolution=300)
def updatepath(self, path, trafo, context):
path.append(closepath())
# The closepath in T1 is different from PostScripts in that it does
# *not* modify the current position; hence we need to add an additional
# moveto here ...
path.append(moveto_pt(*trafo.apply_pt(context.x, context.y)))